The Tutorial will provide an introduction to ontology methods and technology for students and researchers. Topics highlighted in the tutorial will be of particular interest to individuals at institutions conducting clinical and translational research, including institutions which have or are interested in obtaining CTSA (Clinical and Translational Science Award) grants.

The Workshop will provide an opportunity for those involved in ontology-related projects in the field of clinical and translational science to present on-going work and to review what has been achieved thus far. It will conclude with consideration of plans and strategies for enhanced coordination of ontology development initiatives in the field of clinical and translational science in the future.

Changes in biomedical science, public policy, information technology, and electronic heath record (EHR) adoption have converged recently to enable a transformation in the delivery, efficiency, and effectiveness of health care. The true richness and complexity of health records lies within the clinical notes, which are free-text reports written by doctors and nurses in their daily practice. We have developed a scalable annotation and analysis workflow that uses public biomedical ontologies and is based on the term recognition tools developed by the National Center for Biomedical Ontology (NCBO). For further details see here

The principles and practice of data governance, as undertaken across the Mayo Clinic enterprise, will be reviewed and discussed, with particular emphasis on vocabulary harmonization and practice using NCBO tools for research. Extension to larger-scale consortia including the ONC HIT Standards Committee, SHARPn, ISO, and CIMI will be considered.

In i2b2, we are developing methods and tools to help investigators answer research questions using secondary clinical data using a diversity of coded data from billing, decision support, laboratory, and electronic medical records, which can also be combined with data from clinical trials and high-throughput genomic instruments. Looking forward, the coding systems are potentially evolving and changing and yet data will need to be retained in their original coding systems to assure no loss in fidelity. Genomic data has similar challenges from the changing nomenclature and gene coordinates that may alter how similar genetic variants are named over time. We are pursuing a strategy with the National Center for Biomedical Ontology (NCBO) to allow a smooth adaption from one coding system to another so that queries remain valid despite these coding changes. New coding systems and mappings can be presented through NCBO web services, and these are transformed into hierarchies that reflect not only the sibling mappings but also the possibly broader and narrower meanings of the mapped terms.

12:15pm Lunch Break

Afternoon: Major Ontology Initiatives relevant to Clinical and Translational Research

VIVO is a platform for managing researcher profiles at or across institutions in support of research expertise location. Eagle-i is a system that enables researchers to share and search for research resources. ShareCenter facilitates grass-roots sharing of information about expertise, activities, and organizational resources within the CTSAs and related organizations. All of these platforms enable publication of Linked Open Data. We describe the CTSAconnect project to harmonize and develop ontologies from these and other sources to support complex queries regarding expertise and activities of investigators, physicians, biomedical research resources, services, and clinical activities in the translational science domain.

2:00pm Jihad S. Obeid (Medical University of South Carolina): An Ontology for Informed Consents and Other Research Permissions

During the development of a comprehensive system for managing informed consents and permissions for research involving human participants, considerable effort is dedicated to laying down the foundation for a semantic web infrastructure and an underlying ontology to help standardize the development of electronic informed consents and the capture of underlying data. The objective is to allow future connections with other semantic web applications and pooling of data from multiple research projects.

2:45pm Refreshment Break

3:15pm Jessica Tenenbaum (Duke): Ontologies for Omic-Scale Datasets

The use of "omic"-scale biomarkers to enable personalized medicine is becoming an increasingly important facet of translational biomedical research. Ontologies such as the Gene Ontology (GO) and the Ontology for Biomedical Investigations (OBI) can be used to facilitate data sharing, re-use, integration, and querying. This presentation will cover some of the more commonly used ontologies and how they may be applied to these ends.

4:00pm Harold Lehmann (Baltimore): The Human Studies Database (HSDB) and the Ontology of Clinical Research (OCRe)

Current efforts aimed at “tagging” research focus on study execution and results reporting. There is no existing ontology, however, for research methodology. Such an ontology would speed systematic reviews, aid in the assembly of research teams, and enable methodology-based decision support, among other use cases. The Ontology for Clinical Research is a national effort led by Ida Sim from UCSF currently validating its typology and implementing a number of OCRe-based tools. We will contrast this ontology with the Ontology for Biomedical Investigations and with the schemas of ClinicalTrials.gov and BRIDG.

Information about disease pathogenesis and disease course is available almost exclusively as free text and is therefore not easily accessible for query and analysis. We are addressing this problem by developing an ontology-driven NLP system for the mapping of basic pathology knowledge from free text to terms from OBO Foundry ontologies. In particular, we are using the Ontology of General Medical Science, with its tripartite structure of disease-disorder-disease_course, as the basic framework for the system. We will discuss preliminary results and describe planned use cases.

Workshop Day 2: Thursday, April 26 · 8:30am-4:00pm

8:30am Continental Breakfast

EHR, Ontology and Interoperability

9:00am Rob Wynden (UCSF): The CTSA Health Ontology Mapper (HOM).

The CTSA Health Ontology Mapper is an open source project to translate locally encoded patient encounter data, claims data and notes into standard biomedical terminologies by leveraging a real-time integration with the NCBO BioPortal REST services for access to biomedical ontologies and maps.

Numerous problems in the field of ontology are the consequence of (1) failure to pay attention to the instances about which we are collecting data, and (2) the lack of formal mechanisms to track instances and instance data, to relate instance data properly to representational units in ontologies, and to represent all these things unambiguously in the context of EHR data. This presentation will demonstrate Referent Tracking as a solution to these deficiencies with application to various particular use cases such as demographics data.

12:00pm Lunch Break

1:00pm Next Steps

How can we measure the value brought by ontology-based approaches?

How can we ensure high-quality and high-value approaches?

How can we promote a consistent approach to ontology across the CTSA consortium?